
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   36 (  144),  selected   36 , name T0358AL333_2
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358AL333_2.T0358.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    T       2      -       -           -
LGA    Q       3      -       -           -
LGA    S       4      -       -           -
LGA    V       5      -       -           -
LGA    L       6      -       -           -
LGA    L       7      -       -           -
LGA    P       8      -       -           -
LGA    P       9      -       -           -
LGA    G      10      G      10          1.676
LGA    P      11      P      11          2.131
LGA    F      12      F      12          1.312
LGA    Q      16      T      13          1.211
LGA    A      17      R      14          1.692
LGA    Q      18      R      15          1.739
LGA    A      19      Q      16          0.698
LGA    V      20      A      17          0.774
LGA    T      21      Q      18          1.271
LGA    T      22      A      19          0.423
LGA    T      23      V      20          0.976
LGA    Y      24      T      21          1.413
LGA    S      25      T      22          1.240
LGA    N      26      T      23          1.552
LGA    I      27      Y      24          2.247
LGA    T      28      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    L      29      T      28          4.204
LGA    E      30      L      29          4.031
LGA    D      31      -       -           -
LGA    D      32      E      30          2.207
LGA    Q      33      D      31           -
LGA    G      34      D      32           -
LGA    S      35      Q      33           -
LGA    -       -      G      34           -
LGA    H      36      S      35          4.892
LGA    -       -      H      36           -
LGA    -       -      F      37           -
LGA    -       -      R      38           -
LGA    -       -      L      39           -
LGA    -       -      V      40           -
LGA    -       -      V      41           -
LGA    -       -      R      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      V      49           -
LGA    -       -      W      50           -
LGA    -       -      R      51           -
LGA    -       -      A      52           -
LGA    -       -      W      53           -
LGA    F      37      N      54          2.111
LGA    R      38      F      55          2.354
LGA    L      39      E      56          2.698
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    -       -      N      64           -
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   66    5.0     22    2.25    13.64     27.704     0.937

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.212193 * X  +   0.445371 * Y  +   0.869838 * Z  + -167.225616
  Y_new =   0.827109 * X  +  -0.392198 * Y  +   0.402581 * Z  + -45.165237
  Z_new =   0.520447 * X  +   0.804876 * Y  +  -0.285148 * Z  + -38.895000 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.911276   -1.230317  [ DEG:   109.5080    -70.4920 ]
  Theta =  -0.547375   -2.594218  [ DEG:   -31.3623   -148.6377 ]
  Phi   =   1.821929   -1.319664  [ DEG:   104.3888    -75.6112 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0358AL333_2                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL333_2.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   66   5.0   22   2.25   13.64  27.704
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL333_2
REMARK Aligment from pdb entry: 2fok_A
ATOM      1  N   MET     1      -2.988  12.183  18.365  1.00  0.00              
ATOM      2  CA  MET     1      -3.811  11.099  18.865  1.00  0.00              
ATOM      3  C   MET     1      -3.740   9.979  17.826  1.00  0.00              
ATOM      4  O   MET     1      -4.023  10.205  16.650  1.00  0.00              
ATOM      5  N   THR     2      -3.316   8.770  18.234  1.00  0.00              
ATOM      6  CA  THR     2      -3.254   7.695  17.239  1.00  0.00              
ATOM      7  C   THR     2      -4.626   7.497  16.594  1.00  0.00              
ATOM      8  O   THR     2      -5.636   7.404  17.289  1.00  0.00              
ATOM      9  N   GLN     3      -4.662   7.438  15.267  1.00  0.00              
ATOM     10  CA  GLN     3      -5.929   7.271  14.559  1.00  0.00              
ATOM     11  C   GLN     3      -6.296   5.816  14.321  1.00  0.00              
ATOM     12  O   GLN     3      -5.443   4.997  13.994  1.00  0.00              
ATOM     13  N   SER     4      -7.581   5.516  14.499  1.00  0.00              
ATOM     14  CA  SER     4      -8.123   4.178  14.325  1.00  0.00              
ATOM     15  C   SER     4      -8.662   3.980  12.913  1.00  0.00              
ATOM     16  O   SER     4      -9.495   4.762  12.446  1.00  0.00              
ATOM     17  N   VAL     5      -8.183   2.927  12.246  1.00  0.00              
ATOM     18  CA  VAL     5      -8.601   2.599  10.879  1.00  0.00              
ATOM     19  C   VAL     5      -8.940   1.119  10.855  1.00  0.00              
ATOM     20  O   VAL     5      -8.197   0.302  11.390  1.00  0.00              
ATOM     21  N   LEU     6       2.703   1.328   3.071  1.00  0.00              
ATOM     22  CA  LEU     6       3.106   2.699   3.373  1.00  0.00              
ATOM     23  C   LEU     6       3.552   2.790   4.818  1.00  0.00              
ATOM     24  O   LEU     6       4.512   3.489   5.143  1.00  0.00              
ATOM     25  N   LEU     7       2.858   2.067   5.685  1.00  0.00              
ATOM     26  CA  LEU     7       3.192   2.084   7.097  1.00  0.00              
ATOM     27  C   LEU     7       4.594   1.556   7.388  1.00  0.00              
ATOM     28  O   LEU     7       5.450   2.295   7.870  1.00  0.00              
ATOM     29  N   PRO     8       4.848   0.289   7.079  1.00  0.00              
ATOM     30  CA  PRO     8       6.164  -0.273   7.365  1.00  0.00              
ATOM     31  C   PRO     8       7.288   0.187   6.436  1.00  0.00              
ATOM     32  O   PRO     8       8.415  -0.293   6.546  1.00  0.00              
ATOM     33  N   PRO     9       6.995   1.128   5.541  1.00  0.00              
ATOM     34  CA  PRO     9       8.000   1.618   4.602  1.00  0.00              
ATOM     35  C   PRO     9       8.294   3.107   4.740  1.00  0.00              
ATOM     36  O   PRO     9       7.649   3.814   5.523  1.00  0.00              
ATOM     37  N   GLY    10       9.281   3.571   3.973  1.00  0.00              
ATOM     38  CA  GLY    10       9.657   4.977   3.976  1.00  0.00              
ATOM     39  C   GLY    10       9.089   5.672   2.742  1.00  0.00              
ATOM     40  O   GLY    10       7.890   5.560   2.474  1.00  0.00              
ATOM     41  N   PRO    11       9.931   6.395   2.002  1.00  0.00              
ATOM     42  CA  PRO    11       9.498   7.074   0.778  1.00  0.00              
ATOM     43  C   PRO    11       9.456   5.991  -0.308  1.00  0.00              
ATOM     44  O   PRO    11      10.409   5.220  -0.465  1.00  0.00              
ATOM     45  N   PHE    12       8.360   5.937  -1.059  1.00  0.00              
ATOM     46  CA  PHE    12       8.192   4.904  -2.080  1.00  0.00              
ATOM     47  C   PHE    12       7.682   5.430  -3.424  1.00  0.00              
ATOM     48  O   PHE    12       7.034   6.474  -3.495  1.00  0.00              
ATOM     49  N   GLN    16       7.975   4.686  -4.490  1.00  0.00              
ATOM     50  CA  GLN    16       7.506   5.035  -5.828  1.00  0.00              
ATOM     51  C   GLN    16       6.320   4.108  -6.129  1.00  0.00              
ATOM     52  O   GLN    16       6.359   2.920  -5.804  1.00  0.00              
ATOM     53  N   ALA    17       5.268   4.648  -6.742  1.00  0.00              
ATOM     54  CA  ALA    17       4.081   3.855  -7.049  1.00  0.00              
ATOM     55  C   ALA    17       4.427   2.495  -7.625  1.00  0.00              
ATOM     56  O   ALA    17       3.706   1.525  -7.407  1.00  0.00              
ATOM     57  N   GLN    18       5.536   2.423  -8.356  1.00  0.00              
ATOM     58  CA  GLN    18       5.973   1.168  -8.962  1.00  0.00              
ATOM     59  C   GLN    18       6.470   0.178  -7.907  1.00  0.00              
ATOM     60  O   GLN    18       6.355  -1.042  -8.074  1.00  0.00              
ATOM     61  N   ALA    19       7.027   0.700  -6.819  1.00  0.00              
ATOM     62  CA  ALA    19       7.503  -0.161  -5.741  1.00  0.00              
ATOM     63  C   ALA    19       6.285  -0.613  -4.915  1.00  0.00              
ATOM     64  O   ALA    19       6.216  -1.751  -4.454  1.00  0.00              
ATOM     65  N   VAL    20       5.318   0.284  -4.743  1.00  0.00              
ATOM     66  CA  VAL    20       4.106  -0.047  -4.004  1.00  0.00              
ATOM     67  C   VAL    20       3.367  -1.114  -4.793  1.00  0.00              
ATOM     68  O   VAL    20       2.859  -2.078  -4.224  1.00  0.00              
ATOM     69  N   THR    21       3.307  -0.927  -6.108  1.00  0.00              
ATOM     70  CA  THR    21       2.627  -1.872  -6.987  1.00  0.00              
ATOM     71  C   THR    21       3.383  -3.181  -6.919  1.00  0.00              
ATOM     72  O   THR    21       2.792  -4.263  -6.934  1.00  0.00              
ATOM     73  N   THR    22       4.705  -3.061  -6.848  1.00  0.00              
ATOM     74  CA  THR    22       5.592  -4.214  -6.751  1.00  0.00              
ATOM     75  C   THR    22       5.329  -4.981  -5.451  1.00  0.00              
ATOM     76  O   THR    22       5.118  -6.195  -5.468  1.00  0.00              
ATOM     77  N   THR    23       5.350  -4.261  -4.326  1.00  0.00              
ATOM     78  CA  THR    23       5.116  -4.863  -3.014  1.00  0.00              
ATOM     79  C   THR    23       3.721  -5.474  -2.957  1.00  0.00              
ATOM     80  O   THR    23       3.506  -6.507  -2.320  1.00  0.00              
ATOM     81  N   TYR    24       2.776  -4.825  -3.629  1.00  0.00              
ATOM     82  CA  TYR    24       1.401  -5.298  -3.690  1.00  0.00              
ATOM     83  C   TYR    24       1.331  -6.623  -4.454  1.00  0.00              
ATOM     84  O   TYR    24       0.669  -7.575  -4.028  1.00  0.00              
ATOM     85  N   SER    25       2.006  -6.675  -5.596  1.00  0.00              
ATOM     86  CA  SER    25       2.000  -7.885  -6.416  1.00  0.00              
ATOM     87  C   SER    25       2.505  -9.107  -5.633  1.00  0.00              
ATOM     88  O   SER    25       1.963 -10.202  -5.760  1.00  0.00              
ATOM     89  N   ASN    26       3.538  -8.916  -4.823  1.00  0.00              
ATOM     90  CA  ASN    26       4.079 -10.013  -4.040  1.00  0.00              
ATOM     91  C   ASN    26       2.979 -10.665  -3.205  1.00  0.00              
ATOM     92  O   ASN    26       2.999 -11.875  -2.984  1.00  0.00              
ATOM     93  N   ILE    27       2.022  -9.859  -2.749  1.00  0.00              
ATOM     94  CA  ILE    27       0.925 -10.359  -1.930  1.00  0.00              
ATOM     95  C   ILE    27      -0.187 -11.016  -2.734  1.00  0.00              
ATOM     96  O   ILE    27      -1.187 -11.450  -2.174  1.00  0.00              
ATOM     97  N   THR    28      -4.909   2.433 -10.430  1.00  0.00              
ATOM     98  CA  THR    28      -5.921   1.929  -9.513  1.00  0.00              
ATOM     99  C   THR    28      -5.337   2.188  -8.128  1.00  0.00              
ATOM    100  O   THR    28      -6.040   2.616  -7.214  1.00  0.00              
ATOM    101  N   LEU    29      -4.036   1.933  -7.998  1.00  0.00              
ATOM    102  CA  LEU    29      -3.313   2.143  -6.749  1.00  0.00              
ATOM    103  C   LEU    29      -3.285   3.632  -6.401  1.00  0.00              
ATOM    104  O   LEU    29      -3.381   4.001  -5.228  1.00  0.00              
ATOM    105  N   GLU    30      -3.167   4.480  -7.418  1.00  0.00              
ATOM    106  CA  GLU    30      -3.150   5.933  -7.218  1.00  0.00              
ATOM    107  C   GLU    30      -4.516   6.427  -6.729  1.00  0.00              
ATOM    108  O   GLU    30      -4.593   7.314  -5.883  1.00  0.00              
ATOM    109  N   ASP    31      -5.596   5.858  -7.263  1.00  0.00              
ATOM    110  CA  ASP    31      -6.938   6.269  -6.852  1.00  0.00              
ATOM    111  C   ASP    31      -7.240   5.770  -5.447  1.00  0.00              
ATOM    112  O   ASP    31      -7.957   6.417  -4.681  1.00  0.00              
ATOM    113  N   ASP    32      -6.686   4.613  -5.113  1.00  0.00              
ATOM    114  CA  ASP    32      -6.868   4.030  -3.790  1.00  0.00              
ATOM    115  C   ASP    32      -6.160   4.907  -2.750  1.00  0.00              
ATOM    116  O   ASP    32      -6.581   4.986  -1.609  1.00  0.00              
ATOM    117  N   GLN    33       5.690  13.867  -2.984  1.00  0.00              
ATOM    118  CA  GLN    33       6.682  14.816  -3.473  1.00  0.00              
ATOM    119  C   GLN    33       7.185  14.318  -4.817  1.00  0.00              
ATOM    120  O   GLN    33       8.021  13.412  -4.888  1.00  0.00              
ATOM    121  N   GLY    34       6.662  14.905  -5.886  1.00  0.00              
ATOM    122  CA  GLY    34       7.066  14.482  -7.207  1.00  0.00              
ATOM    123  C   GLY    34       6.608  13.055  -7.430  1.00  0.00              
ATOM    124  O   GLY    34       5.410  12.775  -7.419  1.00  0.00              
ATOM    125  N   SER    35       7.560  12.150  -7.613  1.00  0.00              
ATOM    126  CA  SER    35       7.247  10.745  -7.852  1.00  0.00              
ATOM    127  C   SER    35       7.270   9.882  -6.592  1.00  0.00              
ATOM    128  O   SER    35       7.131   8.667  -6.684  1.00  0.00              
ATOM    129  N   HIS    36       7.426  10.497  -5.422  1.00  0.00              
ATOM    130  CA  HIS    36       7.508   9.723  -4.185  1.00  0.00              
ATOM    131  C   HIS    36       6.419   9.962  -3.155  1.00  0.00              
ATOM    132  O   HIS    36       6.028  11.098  -2.883  1.00  0.00              
ATOM    133  N   PHE    37       5.937   8.870  -2.576  1.00  0.00              
ATOM    134  CA  PHE    37       4.907   8.930  -1.555  1.00  0.00              
ATOM    135  C   PHE    37       5.538   8.547  -0.218  1.00  0.00              
ATOM    136  O   PHE    37       6.444   7.713  -0.158  1.00  0.00              
ATOM    137  N   ARG    38       5.052   9.153   0.856  1.00  0.00              
ATOM    138  CA  ARG    38       5.548   8.828   2.181  1.00  0.00              
ATOM    139  C   ARG    38       4.509   9.133   3.240  1.00  0.00              
ATOM    140  O   ARG    38       4.130  10.287   3.420  1.00  0.00              
ATOM    141  N   LEU    39       4.043   8.098   3.935  1.00  0.00              
ATOM    142  CA  LEU    39       3.053   8.293   4.993  1.00  0.00              
ATOM    143  C   LEU    39       3.699   8.989   6.196  1.00  0.00              
ATOM    144  O   LEU    39       4.768   8.592   6.650  1.00  0.00              
END
